Analysis date: 2023-09-18

Depends on

CRC_Xenografts_Batch2_DataProcessing Script

load("../Data/Cache/Xenografts_Batch2_DataProcessing.RData")

TODO

  • Annotated sample prep batch in heatmap

Setup

Load libraries and functions

Analysis

Heatmaps median centered log2 fold change

Phospho-Tyrosines

sample_annotation_df <- tibble( sample = rownames(
  pY_mat_Set1_normtomedian
  ) ) %>% 
   separate(col = sample, sep = "_", 
                   into = c("log2FC", "xenograft", "treatment", 
                            "timepoint", "replicate", "set" ), remove = F) %>%
  column_to_rownames("sample") %>% select(-log2FC)

t(pY_mat_Set1_normtomedian) %>% 
  plot_centered_heatmaply_around_nochange(
    labCol = sub("log2FC_", "", rownames(pY_mat_Set1_normtomedian)),
    col_side_colors = sample_annotation_df)

Phospho-Serines/Threonines

sample_annotation_df <- tibble( sample = rownames(
  pST_mat_Set1_normtomedian
  ) ) %>% 
   separate(col = sample, sep = "_", 
                   into = c("log2FC", "xenograft", "treatment", 
                            "timepoint", "replicate", "set" ), remove = F) %>%
  column_to_rownames("sample") %>% select(-log2FC)

t(pST_mat_Set1_normtomedian) %>% 
  plot_centered_heatmaply_around_nochange(
    labCol = sub("log2FC_", "", rownames(
      pST_mat_Set1_normtomedian
      )),
    col_side_colors = sample_annotation_df)

Session Info

sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] lubridate_1.9.2             forcats_1.0.0              
##  [3] stringr_1.5.0               dplyr_1.1.2                
##  [5] purrr_1.0.2                 readr_2.1.4                
##  [7] tidyr_1.3.0                 tibble_3.2.1               
##  [9] ggplot2_3.4.2               tidyverse_2.0.0            
## [11] mdatools_0.14.0             SummarizedExperiment_1.28.0
## [13] GenomicRanges_1.50.2        GenomeInfoDb_1.34.9        
## [15] MatrixGenerics_1.10.0       matrixStats_1.0.0          
## [17] DEP_1.20.0                  org.Hs.eg.db_3.16.0        
## [19] AnnotationDbi_1.60.2        IRanges_2.32.0             
## [21] S4Vectors_0.36.2            Biobase_2.58.0             
## [23] BiocGenerics_0.44.0         fgsea_1.24.0               
## 
## loaded via a namespace (and not attached):
##   [1] circlize_0.4.15        fastmatch_1.1-3        plyr_1.8.8            
##   [4] igraph_1.5.1           gmm_1.8                lazyeval_0.2.2        
##   [7] shinydashboard_0.7.2   crosstalk_1.2.0        BiocParallel_1.32.6   
##  [10] digest_0.6.33          ca_0.71.1              foreach_1.5.2         
##  [13] htmltools_0.5.6        viridis_0.6.4          fansi_1.0.4           
##  [16] magrittr_2.0.3         memoise_2.0.1          cluster_2.1.4         
##  [19] doParallel_1.0.17      tzdb_0.4.0             limma_3.54.2          
##  [22] ComplexHeatmap_2.14.0  Biostrings_2.66.0      imputeLCMD_2.1        
##  [25] sandwich_3.0-2         timechange_0.2.0       colorspace_2.1-0      
##  [28] blob_1.2.4             xfun_0.40              crayon_1.5.2          
##  [31] RCurl_1.98-1.12        jsonlite_1.8.7         impute_1.72.3         
##  [34] zoo_1.8-12             iterators_1.0.14       glue_1.6.2            
##  [37] hash_2.2.6.2           registry_0.5-1         gtable_0.3.3          
##  [40] zlibbioc_1.44.0        XVector_0.38.0         webshot_0.5.5         
##  [43] GetoptLong_1.0.5       DelayedArray_0.24.0    shape_1.4.6           
##  [46] scales_1.2.1           vsn_3.66.0             mvtnorm_1.2-2         
##  [49] DBI_1.1.3              Rcpp_1.0.11            plotrix_3.8-2         
##  [52] mzR_2.32.0             viridisLite_0.4.2      xtable_1.8-4          
##  [55] clue_0.3-64            bit_4.0.5              preprocessCore_1.60.2 
##  [58] sqldf_0.4-11           MsCoreUtils_1.10.0     DT_0.28               
##  [61] htmlwidgets_1.6.2      httr_1.4.6             gplots_3.1.3          
##  [64] RColorBrewer_1.1-3     ellipsis_0.3.2         farver_2.1.1          
##  [67] pkgconfig_2.0.3        XML_3.99-0.14          sass_0.4.7            
##  [70] utf8_1.2.3             STRINGdb_2.10.1        labeling_0.4.2        
##  [73] reshape2_1.4.4         tidyselect_1.2.0       rlang_1.1.1           
##  [76] later_1.3.1            munsell_0.5.0          tools_4.2.3           
##  [79] cachem_1.0.8           cli_3.6.1              gsubfn_0.7            
##  [82] generics_0.1.3         RSQLite_2.3.1          evaluate_0.21         
##  [85] fastmap_1.1.1          heatmaply_1.4.2        mzID_1.36.0           
##  [88] yaml_2.3.7             knitr_1.43             bit64_4.0.5           
##  [91] caTools_1.18.2         dendextend_1.17.1      KEGGREST_1.38.0       
##  [94] ncdf4_1.21             mime_0.12              compiler_4.2.3        
##  [97] rstudioapi_0.15.0      plotly_4.10.2          png_0.1-8             
## [100] affyio_1.68.0          stringi_1.7.12         bslib_0.5.0           
## [103] MSnbase_2.24.2         lattice_0.21-8         ProtGenerics_1.30.0   
## [106] Matrix_1.6-0           tmvtnorm_1.5           vctrs_0.6.3           
## [109] pillar_1.9.0           norm_1.0-11.1          lifecycle_1.0.3       
## [112] BiocManager_1.30.22    jquerylib_0.1.4        MALDIquant_1.22.1     
## [115] GlobalOptions_0.1.2    data.table_1.14.8      cowplot_1.1.1         
## [118] bitops_1.0-7           seriation_1.5.1        httpuv_1.6.11         
## [121] R6_2.5.1               pcaMethods_1.90.0      affy_1.76.0           
## [124] TSP_1.2-4              promises_1.2.1         gridExtra_2.3         
## [127] KernSmooth_2.23-22     codetools_0.2-19       MASS_7.3-60           
## [130] gtools_3.9.4           assertthat_0.2.1       chron_2.3-61          
## [133] proto_1.0.0            rjson_0.2.21           withr_2.5.0           
## [136] GenomeInfoDbData_1.2.9 parallel_4.2.3         hms_1.1.3             
## [139] grid_4.2.3             rmarkdown_2.23         shiny_1.7.4.1
knitr::knit_exit()